https://github.com/kblin/ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

bioinformatics biology command-line download-genomes genbank genomics ncbi python

Last synced: 30 Mar 2025

https://github.com/bebop/poly

A Go package for engineering organisms.

alignment bioengineering bioinformatics codon-optimizer computational-biology dna dna-barcode dna-barcoding fasta genbank genetic-engineering go golden-gate mash molecular-biology plasmids primer-design sequence-hashing synbio synthetic-biology

Last synced: 05 May 2025

https://github.com/edinburgh-genome-foundry/dnafeaturesviewer

:eye: Python library to plot DNA sequence features (e.g. from Genbank files)

bioinformatics dna-visualization genbank molecular-biology synthetic-biology visualization

Last synced: 14 May 2025

https://github.com/moshi4/pygenomeviz

A genome visualization python package for comparative genomics

bioinformatics comparative-genomics genbank genomics genomics-visualization gff gff3 matplotlib microbial-genomics microbiology python synteny visualization

Last synced: 15 May 2025

https://github.com/pirovc/genome_updater

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

bash bioinformatics database download genbank genome genomes genomics ncbi refseq sequence

Last synced: 11 Apr 2025

https://github.com/mtisza1/Cenote-Taker2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)

annotation cenote-taker2 cenote-unlimited-breadsticks discovery genbank hallmark hhblits hhsearch metagenomes prophage prophage-prediction virome virus virus-discovery virus-evolution virus-sequences

Last synced: 23 Mar 2025

https://github.com/rcs333/VAPiD

VAPiD: Viral Annotation and Identification Pipeline

annotations bioinformatics biology fasta genbank metadata ncbi ngs virology virus

Last synced: 23 Mar 2025

https://github.com/nextstrain/mpox

Nextstrain build for mpox virus

augur auspice bioinformatics genbank genomic-epidemiology metadata monkeypox mpox nextstrain pathogen phylogenetics pipeline virus-evolution

Last synced: 09 May 2025

https://github.com/nextstrain/ncov-ingest

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.

bash genbank gisaid ncov nextstrain pathogen python sars-cov-2

Last synced: 18 Dec 2024

https://github.com/cdcgov/seqsender

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

bioinformatics-pipeline biosample cdc cdc-influenza-division genbank gisaid gisaid-format gisaid-upload gisaid-uploader ncbi-biosamples ncbi-genbank ncbi-sra ncbi-submission ncird ncird-id seqsender sra

Last synced: 13 Apr 2025

https://github.com/koeng101/dnadesign

A Go package for designing DNA.

bioinformatics codon-optimization codon-usage computational-biology dna-barcode dna-folding fasta fastq genbank genetic-engineering go goldengate molecular-biology pileup plasmids rna-folding sam synbio synthetic-biology

Last synced: 13 Apr 2025

https://github.com/cdcgov/tostadas

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

azure bioinformatics conda docker genbank genetics liftoff metadata mpox ncbi nextflow nf-tower pipeline python rna-seq scicomp sequencing singularity sra vadr

Last synced: 15 Apr 2025

https://github.com/moshi4/gbkviz

Easy-to-use web application for visualization and comparison of genomes in Genbank file

bioinformatics biopython comparative-genomics genbank genomics genomics-visualization microbial-genomics python streamlit visualization webapp

Last synced: 21 Jan 2025

https://github.com/dlesl/gb-io

A Rust library for parsing, writing and manipulating Genbank sequence files

biology genbank rust

Last synced: 22 Apr 2025

https://github.com/biojulia/genomicannotations.jl

bioinformatics biology genbank genes genome-annotation gff3 julia

Last synced: 13 Apr 2025

https://github.com/biosustain/goodbye-genbank

A Python package for Biopython that gives feature annotations from GenBank records a new and better life

biopython genbank genomics gff3 sequence-ontology

Last synced: 12 Apr 2025

https://github.com/timothystiles/worst-genbank-ever

The most awful genbank file you'll ever need to parse.

ddbj ensembl genbank genbank-files

Last synced: 28 Mar 2025

https://github.com/j-i-l/genbankparser

Parser (unofficial) for ncbi GenBank data

genbank ncbi parser python2 python3

Last synced: 20 Dec 2024

https://github.com/robaina/genbankpy

Tools to download, parse and filter GenBank files

bioinformatics computational-biology genbank genomics ncbi python sequencing

Last synced: 19 Mar 2025

https://github.com/vbaliga/genbank_downloadr

🔬 Batch downloading of DNA or protein sequences from GenBank

fasta genbank genes purrr r rentrez rstats tidyverse

Last synced: 03 Apr 2025

https://github.com/moltinginstar/addgene-api

An unofficial API for Addgene, the open-source plasmid repository.

addgene api dna dna-sequences genbank plasmids rna snapgene synthetic-biology unofficial web-scraping

Last synced: 11 Apr 2025

https://github.com/pseudogene/uniprime

A workflow-based platform for improved Universal Primer design

bioinformatics genbank pcr primer taxonomy universal-primers

Last synced: 13 Dec 2024

https://github.com/gregyjames/gbtotiny

Genbank to TinyDB.

bioinformatics biology database genbank genomics json tinydb

Last synced: 25 Feb 2025

https://github.com/abhijeetsingh1704/proteincleaner

a python utility to clean PROTEIN sequences and headers

convertion fasta genbank

Last synced: 21 Mar 2025

https://github.com/mdcjansen/dba

DNA barcoding analysis pipeline

ab1 bioinformatics bioinformatics-analysis blastn dna dna-alignment dna-barcode dna-barcoding dna-sequences fasta genbank genbank-files genomics mega11 phylogenetics phylogeny sanger-chromatograms species-identification

Last synced: 11 Mar 2025

https://github.com/gregyjames/genemap

A tool to visualize the genomes of phages.

bioinformatics biology genbank genetics graph

Last synced: 25 Feb 2025

https://github.com/abhijeetsingh1704/subsetseq

a python utility to subset multisequence file based on identifiers from external text file

fasta genbank sequence subset

Last synced: 21 Mar 2025

https://github.com/engkinandatama/ncbi-sequence-fetcher

NCBI Sequence Fetcher is a Python desktop app for downloading nucleotide sequences and extracting metadata from NCBI. It features an easy-to-use GUI, supports FASTA and GenBank formats, and helps researchers students and bioinformaticians efficiently collect DNA sequences and store metadata in Excel files.

academic bioinformatics bioinformatics-tool data-scraping fasta genbank metadata metadata-extraction molecular-biology ncbi nucleotide-sequences python tkinter

Last synced: 13 May 2025